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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.6.dev0

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2018-06-30, 16:12 based on data in:


        General Statistics

        Showing 383/383 rows and 6/7 columns.
        Sample Name% Aligned% Trimmed% Dups% GCLengthM Seqs
        SRR6954498.assembled
        90.1%
        71.7%
        40%
        101 bp
        18.8
        SRR6954498.assembled.bx
        32.4%
        SRR6954498.unassembled
        46.1%
        SRR6954498.unassembled_1
        21.8%
        33%
        49 bp
        29.5
        SRR6954498.unassembled_2
        50.2%
        49%
        150 bp
        29.5
        SRR6954498.unassembled_2.bx
        19.0%
        SRR6954498_1
        83.5%
        32%
        150 bp
        110.6
        SRR6954498_2
        74.9%
        44%
        150 bp
        110.6
        SRR6954499.assembled
        89.9%
        74.0%
        43%
        94 bp
        1.7
        SRR6954499.assembled.bx
        35.4%
        SRR6954499.unassembled
        51.0%
        SRR6954499.unassembled_1
        21.0%
        39%
        52 bp
        1.5
        SRR6954499.unassembled_2
        65.1%
        46%
        151 bp
        1.5
        SRR6954499.unassembled_2.bx
        18.1%
        SRR6954499_1
        68.7%
        34%
        151 bp
        39.4
        SRR6954499_2
        69.5%
        42%
        151 bp
        39.4
        SRR6954500.assembled
        90.5%
        75.8%
        43%
        95 bp
        2.2
        SRR6954500.assembled.bx
        35.0%
        SRR6954500.unassembled
        51.1%
        SRR6954500.unassembled_1
        22.4%
        39%
        51 bp
        1.9
        SRR6954500.unassembled_2
        66.9%
        46%
        151 bp
        1.9
        SRR6954500.unassembled_2.bx
        18.3%
        SRR6954500_1
        68.7%
        34%
        151 bp
        41.2
        SRR6954500_2
        70.7%
        42%
        151 bp
        41.2
        SRR6954501.assembled
        88.8%
        71.2%
        43%
        101 bp
        5.3
        SRR6954501.assembled.bx
        29.8%
        SRR6954501.unassembled
        50.7%
        SRR6954501.unassembled_1
        21.6%
        37%
        57 bp
        6.1
        SRR6954501.unassembled_2
        62.1%
        50%
        151 bp
        6.1
        SRR6954501.unassembled_2.bx
        16.1%
        SRR6954501_1
        72.3%
        35%
        151 bp
        52.3
        SRR6954501_2
        64.2%
        45%
        151 bp
        52.3
        SRR6954502.assembled
        89.7%
        64.0%
        42%
        100 bp
        1.8
        SRR6954502.assembled.bx
        30.8%
        SRR6954502.unassembled
        52.2%
        SRR6954502.unassembled_1
        18.0%
        38%
        58 bp
        2.2
        SRR6954502.unassembled_2
        57.7%
        50%
        151 bp
        2.2
        SRR6954502.unassembled_2.bx
        15.6%
        SRR6954502_1
        67.2%
        36%
        151 bp
        26.0
        SRR6954502_2
        59.9%
        45%
        151 bp
        26.0
        SRR6954503.assembled
        91.0%
        73.7%
        41%
        108 bp
        13.1
        SRR6954503.assembled.bx
        29.7%
        SRR6954503.unassembled
        46.6%
        SRR6954503.unassembled_1
        16.0%
        35%
        49 bp
        38.6
        SRR6954503.unassembled_2
        62.3%
        47%
        150 bp
        38.6
        SRR6954503.unassembled_2.bx
        19.1%
        SRR6954503_1
        85.7%
        33%
        150 bp
        147.3
        SRR6954503_2
        78.2%
        45%
        150 bp
        147.3
        SRR6954504.assembled
        92.2%
        70.5%
        42%
        102 bp
        3.9
        SRR6954504.assembled.bx
        29.1%
        SRR6954504.unassembled
        51.5%
        SRR6954504.unassembled_1
        17.9%
        38%
        54 bp
        7.3
        SRR6954504.unassembled_2
        60.1%
        48%
        150 bp
        7.3
        SRR6954504.unassembled_2.bx
        16.8%
        SRR6954504_1
        67.2%
        34%
        150 bp
        49.1
        SRR6954504_2
        64.6%
        45%
        150 bp
        49.1
        SRR6954505.assembled
        92.1%
        70.9%
        42%
        106 bp
        4.9
        SRR6954505.assembled.bx
        27.7%
        SRR6954505.unassembled
        51.2%
        SRR6954505.unassembled_1
        16.9%
        38%
        54 bp
        9.4
        SRR6954505.unassembled_2
        61.1%
        48%
        150 bp
        9.4
        SRR6954505.unassembled_2.bx
        16.8%
        SRR6954505_1
        69.4%
        34%
        150 bp
        58.2
        SRR6954505_2
        65.5%
        45%
        150 bp
        58.2
        SRR6954506.assembled
        89.8%
        77.9%
        41%
        98 bp
        19.1
        SRR6954506.assembled.bx
        31.5%
        SRR6954506.unassembled
        52.7%
        SRR6954506.unassembled_1
        27.6%
        36%
        51 bp
        15.8
        SRR6954506.unassembled_2
        66.0%
        48%
        150 bp
        15.8
        SRR6954506.unassembled_2.bx
        18.3%
        SRR6954506_1
        83.0%
        32%
        150 bp
        82.4
        SRR6954506_2
        77.6%
        42%
        150 bp
        82.4
        SRR6954507.assembled
        81.7%
        75.9%
        42%
        98 bp
        27.6
        SRR6954507.assembled.bx
        36.1%
        SRR6954507.unassembled
        44.1%
        SRR6954507.unassembled_1
        25.2%
        39%
        52 bp
        60.8
        SRR6954507.unassembled_2
        64.7%
        49%
        151 bp
        60.8
        SRR6954507.unassembled_2.bx
        18.2%
        SRR6954507_1
        83.6%
        34%
        151 bp
        166.3
        SRR6954507_2
        75.6%
        45%
        151 bp
        166.3
        SRR6954508.assembled
        90.7%
        67.6%
        42%
        114 bp
        6.3
        SRR6954508.assembled.bx
        29.4%
        SRR6954508.unassembled
        51.5%
        SRR6954508.unassembled_1
        17.6%
        38%
        51 bp
        17.4
        SRR6954508.unassembled_2
        69.2%
        48%
        150 bp
        17.4
        SRR6954508.unassembled_2.bx
        18.3%
        SRR6954508_1
        70.3%
        33%
        150 bp
        84.4
        SRR6954508_2
        78.6%
        45%
        150 bp
        84.4
        SRR6954509.assembled
        92.3%
        78.7%
        42%
        104 bp
        27.7
        SRR6954509.assembled.bx
        31.9%
        SRR6954509.unassembled
        51.3%
        SRR6954509.unassembled_1
        26.8%
        38%
        53 bp
        38.7
        SRR6954509.unassembled_2
        71.9%
        50%
        151 bp
        38.7
        SRR6954509.unassembled_2.bx
        17.4%
        SRR6954509_1
        85.6%
        33%
        151 bp
        176.1
        SRR6954509_2
        78.5%
        45%
        151 bp
        176.1
        SRR6954510.assembled
        36.7%
        72.0%
        40%
        62 bp
        19.3
        SRR6954510.assembled.bx
        55.1%
        SRR6954510.unassembled
        36.4%
        SRR6954510.unassembled_1
        54.5%
        37%
        25 bp
        9.0
        SRR6954510.unassembled_2
        30.9%
        46%
        150 bp
        9.0
        SRR6954510.unassembled_2.bx
        28.8%
        SRR6954510_1
        81.4%
        31%
        150 bp
        105.4
        SRR6954510_2
        71.7%
        38%
        150 bp
        105.4
        SRR6954511.assembled
        92.5%
        62.8%
        41%
        100 bp
        1.7
        SRR6954511.assembled.bx
        32.5%
        SRR6954511.unassembled
        47.7%
        SRR6954511.unassembled_1
        10.6%
        37%
        49 bp
        5.3
        SRR6954511.unassembled_2
        53.9%
        50%
        150 bp
        5.3
        SRR6954511.unassembled_2.bx
        18.7%
        SRR6954511_1
        71.8%
        33%
        150 bp
        45.1
        SRR6954511_2
        73.7%
        47%
        150 bp
        45.1
        SRR6954530.assembled
        93.7%
        70.7%
        39%
        110 bp
        5.9
        SRR6954530.assembled.bx
        29.8%
        SRR6954530.unassembled
        51.5%
        SRR6954530.unassembled_1
        14.7%
        35%
        50 bp
        19.7
        SRR6954530.unassembled_2
        66.9%
        45%
        150 bp
        19.7
        SRR6954530.unassembled_2.bx
        18.4%
        SRR6954530_1
        76.6%
        32%
        150 bp
        96.3
        SRR6954530_2
        82.4%
        43%
        150 bp
        96.3
        SRR6954531.assembled
        82.0%
        63.1%
        39%
        96 bp
        8.9
        SRR6954531.assembled.bx
        35.8%
        SRR6954531.unassembled
        46.2%
        SRR6954531.unassembled_1
        18.0%
        32%
        46 bp
        12.3
        SRR6954531.unassembled_2
        42.6%
        48%
        150 bp
        12.3
        SRR6954531.unassembled_2.bx
        20.2%
        SRR6954531_1
        81.5%
        30%
        150 bp
        88.7
        SRR6954531_2
        74.7%
        41%
        150 bp
        88.7
        SRR6954532.assembled
        78.2%
        48.8%
        41%
        88 bp
        0.3
        SRR6954532.assembled.bx
        34.6%
        SRR6954532.unassembled
        45.9%
        SRR6954532.unassembled_1
        7.6%
        35%
        51 bp
        0.3
        SRR6954532.unassembled_2
        32.2%
        49%
        151 bp
        0.3
        SRR6954532.unassembled_2.bx
        18.3%
        SRR6954532_1
        62.0%
        35%
        151 bp
        22.5
        SRR6954532_2
        56.0%
        44%
        151 bp
        22.5
        SRR6954533.assembled
        89.8%
        75.1%
        42%
        99 bp
        25.0
        SRR6954533.assembled.bx
        31.5%
        SRR6954533.unassembled
        48.5%
        SRR6954533.unassembled_1
        22.9%
        38%
        49 bp
        22.3
        SRR6954533.unassembled_2
        64.1%
        49%
        150 bp
        22.3
        SRR6954533.unassembled_2.bx
        19.0%
        SRR6954533_1
        84.9%
        35%
        150 bp
        115.7
        SRR6954533_2
        72.3%
        44%
        150 bp
        115.7
        SRR6954534.assembled
        86.9%
        67.2%
        43%
        116 bp
        11.3
        SRR6954534.assembled.bx
        29.6%
        SRR6954534.unassembled
        51.0%
        SRR6954534.unassembled_1
        23.2%
        40%
        48 bp
        26.2
        SRR6954534.unassembled_2
        66.3%
        48%
        150 bp
        26.2
        SRR6954534.unassembled_2.bx
        19.5%
        SRR6954534_1
        82.3%
        33%
        150 bp
        101.9
        SRR6954534_2
        75.5%
        45%
        150 bp
        101.9
        SRR6954535.assembled
        92.5%
        67.2%
        45%
        120 bp
        6.4
        SRR6954535.assembled.bx
        25.6%
        SRR6954535.unassembled
        50.8%
        SRR6954535.unassembled_1
        15.8%
        44%
        54 bp
        19.5
        SRR6954535.unassembled_2
        64.2%
        50%
        150 bp
        19.5
        SRR6954535.unassembled_2.bx
        16.8%
        SRR6954535_1
        73.3%
        36%
        150 bp
        89.7
        SRR6954535_2
        75.9%
        47%
        150 bp
        89.7
        SRR6954538.assembled
        95.4%
        88.4%
        38%
        108 bp
        5.2
        SRR6954538.assembled.bx
        26.3%
        SRR6954538.unassembled
        52.3%
        SRR6954538.unassembled_1
        23.3%
        30%
        54 bp
        10.1
        SRR6954538.unassembled_2
        83.3%
        44%
        150 bp
        10.1
        SRR6954538.unassembled_2.bx
        16.9%
        SRR6954538_1
        69.0%
        31%
        150 bp
        69.8
        SRR6954538_2
        86.3%
        41%
        150 bp
        69.8
        SRR6954539.assembled
        91.1%
        88.3%
        37%
        110 bp
        8.9
        SRR6954539.assembled.bx
        25.4%
        SRR6954539.unassembled
        53.2%
        SRR6954539.unassembled_1
        34.7%
        30%
        58 bp
        16.7
        SRR6954539.unassembled_2
        79.2%
        44%
        151 bp
        16.7
        SRR6954539.unassembled_2.bx
        15.4%
        SRR6954539_1
        73.4%
        33%
        151 bp
        70.5
        SRR6954539_2
        80.5%
        42%
        151 bp
        70.5
        SRR6954540.assembled
        80.2%
        69.4%
        37%
        71 bp
        28.8
        SRR6954540.assembled.bx
        52.7%
        SRR6954540.unassembled
        43.4%
        SRR6954540.unassembled_1
        49.2%
        31%
        23 bp
        22.3
        SRR6954540.unassembled_2
        40.9%
        48%
        150 bp
        22.3
        SRR6954540.unassembled_2.bx
        29.6%
        SRR6954540_1
        77.9%
        26%
        150 bp
        126.8
        SRR6954540_2
        75.4%
        37%
        150 bp
        126.8
        SRR6954543.assembled
        91.7%
        70.1%
        41%
        102 bp
        5.2
        SRR6954543.assembled.bx
        30.0%
        SRR6954543.unassembled
        48.6%
        SRR6954543.unassembled_1
        22.7%
        33%
        50 bp
        7.8
        SRR6954543.unassembled_2
        49.1%
        49%
        150 bp
        7.8
        SRR6954543.unassembled_2.bx
        18.5%
        SRR6954543_1
        75.1%
        33%
        150 bp
        56.2
        SRR6954543_2
        68.9%
        45%
        150 bp
        56.2
        SRR6954544.assembled
        90.0%
        72.4%
        41%
        99 bp
        16.7
        SRR6954544.assembled.bx
        31.9%
        SRR6954544.unassembled
        47.4%
        SRR6954544.unassembled_1
        19.2%
        32%
        48 bp
        21.4
        SRR6954544.unassembled_2
        54.2%
        49%
        150 bp
        21.4
        SRR6954544.unassembled_2.bx
        19.5%
        SRR6954544_1
        85.9%
        32%
        150 bp
        94.4
        SRR6954544_2
        71.0%
        44%
        150 bp
        94.4
        SRR6954545.assembled
        86.3%
        59.4%
        42%
        97 bp
        1.1
        SRR6954545.assembled.bx
        31.1%
        SRR6954545.unassembled
        50.1%
        SRR6954545.unassembled_1
        15.1%
        35%
        52 bp
        1.8
        SRR6954545.unassembled_2
        49.9%
        49%
        150 bp
        1.8
        SRR6954545.unassembled_2.bx
        17.5%
        SRR6954545_1
        63.9%
        35%
        150 bp
        25.2
        SRR6954545_2
        60.2%
        45%
        150 bp
        25.2
        SRR6954546.assembled
        90.5%
        63.7%
        42%
        101 bp
        2.2
        SRR6954546.assembled.bx
        29.6%
        SRR6954546.unassembled
        50.6%
        SRR6954546.unassembled_1
        15.7%
        36%
        54 bp
        3.8
        SRR6954546.unassembled_2
        56.4%
        50%
        150 bp
        3.8
        SRR6954546.unassembled_2.bx
        17.0%
        SRR6954546_1
        66.8%
        35%
        150 bp
        28.4
        SRR6954546_2
        63.1%
        46%
        150 bp
        28.4
        SRR6954548.assembled
        91.6%
        71.4%
        43%
        105 bp
        3.3
        SRR6954548.assembled.bx
        27.1%
        SRR6954548.unassembled
        44.1%
        SRR6954548.unassembled_1
        14.3%
        37%
        56 bp
        5.9
        SRR6954548.unassembled_2
        42.2%
        53%
        150 bp
        5.9
        SRR6954548.unassembled_2.bx
        15.9%
        SRR6954548_1
        64.6%
        34%
        150 bp
        46.3
        SRR6954548_2
        67.3%
        48%
        150 bp
        46.3
        SRR6954560.assembled
        91.0%
        74.5%
        40%
        105 bp
        31.5
        SRR6954560.assembled.bx
        29.7%
        SRR6954560.unassembled
        45.9%
        SRR6954560.unassembled_1
        21.8%
        33%
        49 bp
        38.0
        SRR6954560.unassembled_2
        51.7%
        48%
        150 bp
        38.0
        SRR6954560.unassembled_2.bx
        19.0%
        SRR6954560_1
        87.9%
        32%
        150 bp
        142.9
        SRR6954560_2
        77.5%
        43%
        150 bp
        142.9
        SRR6954561.assembled
        91.5%
        53.5%
        40%
        116 bp
        1.1
        SRR6954561.assembled.bx
        26.7%
        SRR6954561.unassembled
        50.5%
        SRR6954561.unassembled_1
        10.8%
        34%
        53 bp
        3.6
        SRR6954561.unassembled_2
        57.1%
        48%
        150 bp
        3.6
        SRR6954561.unassembled_2.bx
        17.3%
        SRR6954561_1
        68.7%
        32%
        150 bp
        36.0
        SRR6954561_2
        76.3%
        46%
        150 bp
        36.0
        SRR6954562.assembled
        90.5%
        73.9%
        42%
        100 bp
        15.5
        SRR6954562.assembled.bx
        31.7%
        SRR6954562.unassembled
        49.3%
        SRR6954562.unassembled_1
        17.2%
        38%
        51 bp
        25.3
        SRR6954562.unassembled_2
        68.4%
        51%
        150 bp
        25.3
        SRR6954562.unassembled_2.bx
        18.2%
        SRR6954562_1
        82.1%
        34%
        150 bp
        166.5
        SRR6954562_2
        77.8%
        46%
        150 bp
        166.5
        SRR6954563.assembled
        86.8%
        66.1%
        42%
        107 bp
        5.6
        SRR6954563.assembled.bx
        29.0%
        SRR6954563.unassembled
        46.7%
        SRR6954563.unassembled_1
        14.4%
        33%
        50 bp
        13.2
        SRR6954563.unassembled_2
        60.2%
        49%
        150 bp
        13.2
        SRR6954563.unassembled_2.bx
        18.5%
        SRR6954563_1
        84.8%
        33%
        150 bp
        47.2
        SRR6954563_2
        66.5%
        45%
        150 bp
        47.2
        SRR6954564.assembled
        91.0%
        68.7%
        41%
        104 bp
        3.8
        SRR6954564.assembled.bx
        30.9%
        SRR6954564.unassembled
        48.2%
        SRR6954564.unassembled_1
        13.2%
        38%
        48 bp
        11.6
        SRR6954564.unassembled_2
        61.4%
        47%
        150 bp
        11.6
        SRR6954564.unassembled_2.bx
        19.4%
        SRR6954564_1
        76.7%
        32%
        150 bp
        51.4
        SRR6954564_2
        78.8%
        45%
        150 bp
        51.4
        SRR6954565.assembled
        89.7%
        60.2%
        42%
        117 bp
        2.9
        SRR6954565.assembled.bx
        28.5%
        SRR6954565.unassembled
        50.8%
        SRR6954565.unassembled_1
        15.3%
        35%
        51 bp
        12.9
        SRR6954565.unassembled_2
        62.5%
        49%
        150 bp
        12.9
        SRR6954565.unassembled_2.bx
        18.0%
        SRR6954565_1
        76.0%
        32%
        150 bp
        63.5
        SRR6954565_2
        70.9%
        47%
        150 bp
        63.5
        SRR6954566.assembled
        87.9%
        45.9%
        42%
        95 bp
        0.3
        SRR6954566.assembled.bx
        31.7%
        SRR6954566.unassembled
        48.5%
        SRR6954566.unassembled_1
        10.9%
        36%
        52 bp
        0.3
        SRR6954566.unassembled_2
        34.8%
        49%
        151 bp
        0.3
        SRR6954566.unassembled_2.bx
        17.8%
        SRR6954566_1
        53.5%
        33%
        151 bp
        25.8
        SRR6954566_2
        58.0%
        43%
        151 bp
        25.8
        SRR6954567.assembled
        86.9%
        51.2%
        42%
        94 bp
        0.5
        SRR6954567.assembled.bx
        32.5%
        SRR6954567.unassembled
        48.5%
        SRR6954567.unassembled_1
        11.3%
        36%
        53 bp
        0.5
        SRR6954567.unassembled_2
        38.6%
        49%
        151 bp
        0.5
        SRR6954567.unassembled_2.bx
        17.6%
        SRR6954567_1
        54.0%
        34%
        151 bp
        25.9
        SRR6954567_2
        56.2%
        43%
        151 bp
        25.9
        SRR6954568.assembled
        80.2%
        62.4%
        43%
        97 bp
        1.3
        SRR6954568.assembled.bx
        30.9%
        SRR6954568.unassembled
        50.1%
        SRR6954568.unassembled_1
        11.5%
        37%
        60 bp
        2.1
        SRR6954568.unassembled_2
        60.7%
        50%
        151 bp
        2.1
        SRR6954568.unassembled_2.bx
        14.9%
        SRR6954568_1
        61.5%
        37%
        151 bp
        33.9
        SRR6954568_2
        57.0%
        46%
        151 bp
        33.9
        SRR6954572.assembled
        91.6%
        79.5%
        43%
        109 bp
        15.1
        SRR6954572.assembled.bx
        27.7%
        SRR6954572.unassembled
        52.9%
        SRR6954572.unassembled_1
        26.0%
        38%
        55 bp
        33.8
        SRR6954572.unassembled_2
        76.9%
        49%
        150 bp
        33.8
        SRR6954572.unassembled_2.bx
        16.5%
        SRR6954572_1
        86.4%
        34%
        150 bp
        148.4
        SRR6954572_2
        80.5%
        45%
        150 bp
        148.4
        SRR6954573.assembled
        88.0%
        71.9%
        42%
        94 bp
        6.4
        SRR6954573.assembled.bx
        35.7%
        SRR6954573.unassembled
        51.8%
        SRR6954573.unassembled_1
        26.9%
        39%
        55 bp
        6.3
        SRR6954573.unassembled_2
        63.0%
        49%
        151 bp
        6.3
        SRR6954573.unassembled_2.bx
        16.9%
        SRR6954573_1
        69.3%
        33%
        151 bp
        51.6
        SRR6954573_2
        65.3%
        43%
        151 bp
        51.6
        SRR6954574.assembled
        90.3%
        72.6%
        42%
        99 bp
        5.1
        SRR6954574.assembled.bx
        32.0%
        SRR6954574.unassembled
        51.6%
        SRR6954574.unassembled_1
        24.5%
        39%
        55 bp
        5.3
        SRR6954574.unassembled_2
        62.1%
        49%
        151 bp
        5.3
        SRR6954574.unassembled_2.bx
        16.6%
        SRR6954574_1
        68.6%
        34%
        151 bp
        42.9
        SRR6954574_2
        65.9%
        43%
        151 bp
        42.9
        SRR6954575.assembled
        89.5%
        66.6%
        42%
        113 bp
        12.7
        SRR6954575.assembled.bx
        28.5%
        SRR6954575.unassembled
        47.8%
        SRR6954575.unassembled_1
        14.6%
        33%
        50 bp
        43.9
        SRR6954575.unassembled_2
        59.1%
        49%
        150 bp
        43.9
        SRR6954575.unassembled_2.bx
        18.4%
        SRR6954575_1
        84.9%
        32%
        150 bp
        160.6
        SRR6954575_2
        77.2%
        46%
        150 bp
        160.6
        SRR6954576.assembled
        91.6%
        73.2%
        43%
        116 bp
        14.3
        SRR6954576.assembled.bx
        27.2%
        SRR6954576.unassembled
        48.6%
        SRR6954576.unassembled_1
        16.7%
        36%
        55 bp
        51.4
        SRR6954576.unassembled_2
        62.9%
        49%
        150 bp
        51.4
        SRR6954576.unassembled_2.bx
        16.4%
        SRR6954576_1
        85.6%
        34%
        150 bp
        150.6
        SRR6954576_2
        79.6%
        47%
        150 bp
        150.6
        SRR6954577.assembled
        92.9%
        71.3%
        42%
        107 bp
        19.0
        SRR6954577.assembled.bx
        27.6%
        SRR6954577.unassembled
        50.1%
        SRR6954577.unassembled_1
        16.5%
        37%
        54 bp
        49.8
        SRR6954577.unassembled_2
        68.9%
        50%
        150 bp
        49.8
        SRR6954577.unassembled_2.bx
        17.0%
        SRR6954577_1
        87.0%
        35%
        150 bp
        180.7
        SRR6954577_2
        78.9%
        47%
        150 bp
        180.7
        SRR6954578.assembled
        89.4%
        58.7%
        43%
        122 bp
        10.7
        SRR6954578.assembled.bx
        27.9%
        SRR6954578.unassembled
        49.8%
        SRR6954578.unassembled_1
        18.0%
        35%
        47 bp
        56.9
        SRR6954578.unassembled_2
        58.6%
        50%
        150 bp
        56.9
        SRR6954578.unassembled_2.bx
        19.6%
        SRR6954578_1
        83.7%
        32%
        150 bp
        92.1
        SRR6954578_2
        69.1%
        48%
        150 bp
        92.1
        SRR6954579.assembled
        88.2%
        65.8%
        40%
        111 bp
        13.0
        SRR6954579.assembled.bx
        31.7%
        SRR6954579.unassembled
        47.2%
        SRR6954579.unassembled_1
        24.3%
        36%
        47 bp
        29.1
        SRR6954579.unassembled_2
        54.8%
        47%
        151 bp
        29.1
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        20.1%
        SRR6954579_1
        84.5%
        31%
        151 bp
        180.2
        SRR6954579_2
        76.3%
        43%
        151 bp
        180.2
        SRR6954580.assembled
        58.0%
        41%
        119 bp
        2.4
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        25.4%
        SRR6954580.unassembled_1
        12.0%
        35%
        52 bp
        6.9
        SRR6954580.unassembled_2
        59.1%
        48%
        150 bp
        6.9
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        17.6%
        SRR6954580_1
        81.5%
        34%
        150 bp
        29.2
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        69.6%
        45%
        150 bp
        29.2
        SRR6954582.assembled
        92.4%
        71.9%
        40%
        111 bp
        29.5
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        27.0%
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        46.9%
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        20.0%
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        49.3
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        48.8%
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        49.3
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        17.6%
        SRR6954582_1
        90.2%
        32%
        150 bp
        137.1
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        74.7%
        44%
        150 bp
        137.1
        SRR6954799.assembled
        92.3%
        64.4%
        41%
        119 bp
        4.9
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        25.4%
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        53.0%
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        15.3%
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        55 bp
        5.0
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        60.4%
        48%
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        5.0
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        16.5%
        SRR6954799_1
        69.6%
        33%
        150 bp
        56.0
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        71.5%
        43%
        150 bp
        56.0

        HISAT2

        HISAT2 is a fast and sensitive alignment program for mapping NGS reads (both DNA and RNA) against a reference genome or population of reference genomes.

        loading..

        Please note that single mate alignment counts are halved to tally with pair counts properly.

        loading..

        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        This plot shows the number of reads with certain lengths of adapter trimmed. Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length. See the cutadapt documentation for more information on how these numbers are generated.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).